› 5oxv

X-ray diffraction
6.72Å resolution

Structure of the 4_601_157 tetranucleosome (C2 form)

Released:
DOI: 10.2210/pdb5oxv/pdb
PDB entry 5oxv coloured by chain, front view.
PDB entry 5oxv coloured by chain, side view.
PDB entry 5oxv coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Capturing Structural Heterogeneity in Chromatin Fibers.
Ekundayo B, Richmond TJ, Schalch T
J Mol Biol 429 3031-3042 (2017)
PMID: 28893533

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119119 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H2B 1.1 Chains: D, H, N, R
Molecule details ›
Chains: D, H, N, R
Length: 126 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H2A type 1 Chains: C, G, M, Q
Molecule details ›
Chains: C, G, M, Q
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Histone H4 Chains: B, F, L, P
Molecule details ›
Chains: B, F, L, P
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H3.2 Chains: A, E, K, O
Molecule details ›
Chains: A, E, K, O
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
DNA STRAND 1 (601-based sequence model) Chain: J
Molecule details ›
Chain: J
Length: 312 nucleotides
Theoretical weight: 96.89 KDa
DNA STRAND 2 (601-based sequence model) Chain: I
Molecule details ›
Chain: I
Length: 313 nucleotides
Theoretical weight: 96.15 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2
Unit cell:
a: 348.839Å b: 63.274Å c: 271.361Å
α: 90° β: 124.74° γ: 90°
R-values:
R R work R free
0.321 0.317 0.352
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Biophysics of Chromatin Dynamics.
Fierz et al. (2019)
8 more

2 mentions without citation

Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1.
Pluta et al. (2022)
1 more